[gmx-users] Simulation of membrane protein
jmsstarlight at gmail.com
Sun Oct 16 08:55:38 CEST 2011
In the algorthm presented in the tutorial there is one inconvenience that is
many iterations of the shrinking/minimization of the protein ( e.g if i'd
like to obrain good value for S per lipid for my structure). Is there any
way to make this process automated ? ( e.g some program wich could do all of
those operations untill defined value for some magnitudes would be reached )
Also I'd like to ask about g_membed. As I've understood for that program I
need in merged pdb struture ( consist of my peptide inserted in the membrane
) as well as merged topology. Is there any way to prepare this data exept
the way presented in your tutorial ? (
E.g I've heard that this could also be done via PyMol. Where I could find
example of such preparation ?
Thanks for your help,
2011/10/15 Justin A. Lemkul <jalemkul at vt.edu>
> James Starlight wrote:
>> Dear Gromacs's users!
>> I'd like to simulate some membrane proteins in their native environment.
>> Recently I've found a good tutotial of the same simulation of the KALP
>> peptide in DPPC membrane (http://www.bevanlab.biochem.**
>> Is there someone who have also tried to make thit tutorial ?
> Yes, per our server logs, several hundred people have :)
> First of all its very intresting for me the positioning of the protein in
>> the membrane via specific perl script called infrategro. What values for
>> the cutoff radius as well as measurements of the area per lipid are most
>> adequate for different membrane proteins?
> The ones given in the tutorial work quite well. They are the defaults
> suggested by the developers of InflateGRO.
> Could you also tell me some alternative ways of full algorithm of the
>> protein insertion in the membrane?
> Careful use of genbox (but will require significantly more equilibration as
> there will be large gaps), or g_membed.
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users